Plot flag percentages, or map flagged records

Without grouping, one horizontal bar per test of a rule: the full bar is the share of records the test flags, the dark part the share it is the only reason for. With grouping (by or bins in tally_flags()), a grid of tests by groups shaded and labelled with the share each test flags in each group. type = "map" on a flagged data frame draws the records over the Natural Earth land, coloured by whether the rule removes them.

Usage

# S3 method for class 'occ_summary'
plot(x, rule = NULL, ...)

# S3 method for class 'occ_tally'
plot(x, rule = NULL, ...)

# S3 method for class 'occ_flags'
plot(x, type = c("tests", "map"), rules = NULL, xlim = NULL, ylim = NULL, ...)

# S3 method for class 'occ_flagged'
plot(x, rules = NULL, ...)

Arguments

x

A flagged data frame (occ_flags), an occ_flagged object, an occ_tally or an occ_summary.

rule

Name of the rule to draw. Default: the first rule.

...

For occ_flags and occ_flagged: passed to tally_flags() (by, bins, tests). Otherwise unused.

type

For a flagged data frame: "tests" (the shares, as for an occ_summary) or "map".

rules

Named list of rules, as in tally_flags(). For type = "map" the first rule decides which records are drawn as removed. Default: one rule holding every test run.

xlim, ylim

For type = "map": longitude and latitude limits of the map. Default: the extent of the records. The title counts the records inside the limits.

Value

x, invisibly.

Examples

x <- data.frame(species = c("a", "a", "b", "c", "c"),
                kingdom = c("P", "P", "A", "A", "A"),
                decimalLongitude = c(12.58, 0, 16.37, 2.35, 2.35),
                decimalLatitude = c(55.67, 0, 48.21, 48.85, 48.85))
f <- flag_occurrences(x)
plot(f)
plot(f, by = "kingdom")
plot(f, type = "map")
plot(f, type = "map", xlim = c(0, 20), ylim = c(45, 60))